HEADER PROTEIN TURNOVER/ENDOCYTOSIS 29-DEC-05 2FIF
TITLE CRYSTAL STRUCTURE OF A BOVINE RABEX-5 FRAGMENT COMPLEXED WITH
TITLE 2 UBIQUITIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: UBIQUITIN;
COMPND 3 CHAIN: A, C, E;
COMPND 4 MOL_ID: 2;
COMPND 5 MOLECULE: RAB5 GDP/GTP EXCHANGE FACTOR;
COMPND 6 CHAIN: B, D, F;
COMPND 7 FRAGMENT: A20 ZINC FINGER AND INVERTED UBIQUITIN INTERACTING MOTIF
COMPND 8 DOMAINS;
COMPND 9 SYNONYM: RABEX-5;
COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS;
SOURCE 3 ORGANISM_COMMON: CATTLE;
SOURCE 4 ORGANISM_TAXID: 9913;
SOURCE 5 MOL_ID: 2;
SOURCE 6 ORGANISM_SCIENTIFIC: BOS TAURUS;
SOURCE 7 ORGANISM_COMMON: CATTLE;
SOURCE 8 ORGANISM_TAXID: 9913;
SOURCE 9 GENE: RABGEF1, RABEX5;
SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PARALLEL GST2
KEYWDS ZINC FINGER, HELIX, PROTEIN TURNOVER-ENDOCYTOSIS COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR S.LEE,J.H.HURLEY
REVDAT 5 30-AUG-23 2FIF 1 REMARK SEQADV LINK
REVDAT 4 13-JUL-11 2FIF 1 VERSN
REVDAT 3 24-FEB-09 2FIF 1 VERSN
REVDAT 2 21-MAR-06 2FIF 1 JRNL
REVDAT 1 07-FEB-06 2FIF 0
JRNL AUTH S.LEE,Y.C.TSAI,R.MATTERA,W.J.SMITH,M.S.KOSTELANSKY,
JRNL AUTH 2 A.M.WEISSMAN,J.S.BONIFACINO,J.H.HURLEY
JRNL TITL STRUCTURAL BASIS FOR UBIQUITIN RECOGNITION AND
JRNL TITL 2 AUTOUBIQUITINATION BY RABEX-5
JRNL REF NAT.STRUCT.MOL.BIOL. V. 13 264 2006
JRNL REFN ISSN 1545-9993
JRNL PMID 16462746
JRNL DOI 10.1038/NSMB1064
REMARK 2
REMARK 2 RESOLUTION. 2.49 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0005
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.49
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 90.91
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9
REMARK 3 NUMBER OF REFLECTIONS : 18271
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.230
REMARK 3 R VALUE (WORKING SET) : 0.228
REMARK 3 FREE R VALUE : 0.263
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 985
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.49
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1137
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.09
REMARK 3 BIN R VALUE (WORKING SET) : 0.3210
REMARK 3 BIN FREE R VALUE SET COUNT : 61
REMARK 3 BIN FREE R VALUE : 0.4680
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3201
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 8
REMARK 3 SOLVENT ATOMS : 19
REMARK 3
REMARK 3 B VALUES.
REMARK 3 B VALUE TYPE : LIKELY RESIDUAL
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.20
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -1.17000
REMARK 3 B22 (A**2) : 0.90000
REMARK 3 B33 (A**2) : 0.14000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -0.21000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.453
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.283
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.208
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.649
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3262 ; 0.007 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4382 ; 0.991 ; 1.965
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 386 ; 4.750 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;35.839 ;25.207
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 636 ;16.527 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;16.682 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 464 ; 0.070 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2451 ; 0.002 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1315 ; 0.178 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2194 ; 0.295 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 92 ; 0.132 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 61 ; 0.195 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.128 ; 0.200
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2011 ; 0.245 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3124 ; 0.426 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1432 ; 0.688 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1258 ; 1.077 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 9
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 1 A 73
REMARK 3 ORIGIN FOR THE GROUP (A): 143.6409 6.3544 10.4229
REMARK 3 T TENSOR
REMARK 3 T11: -0.2448 T22: -0.3859
REMARK 3 T33: -0.2660 T12: -0.0014
REMARK 3 T13: -0.0039 T23: -0.0354
REMARK 3 L TENSOR
REMARK 3 L11: 3.0870 L22: 6.3617
REMARK 3 L33: 6.5466 L12: 1.6437
REMARK 3 L13: -0.1583 L23: -2.0602
REMARK 3 S TENSOR
REMARK 3 S11: 0.1104 S12: -0.2968 S13: 0.1097
REMARK 3 S21: 0.4605 S22: -0.0275 S23: 0.0607
REMARK 3 S31: -0.1676 S32: 0.1288 S33: -0.0829
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : C 1 C 73
REMARK 3 ORIGIN FOR THE GROUP (A): 117.1598 -3.2328 15.9929
REMARK 3 T TENSOR
REMARK 3 T11: -0.1540 T22: 0.0422
REMARK 3 T33: 0.0239 T12: 0.0461
REMARK 3 T13: 0.0182 T23: 0.0405
REMARK 3 L TENSOR
REMARK 3 L11: 15.6228 L22: 7.0593
REMARK 3 L33: 8.5124 L12: -2.4764
REMARK 3 L13: -7.5349 L23: -1.2880
REMARK 3 S TENSOR
REMARK 3 S11: -0.0292 S12: -0.2359 S13: 0.8121
REMARK 3 S21: -0.1707 S22: 0.4635 S23: 0.8744
REMARK 3 S31: -0.2533 S32: -0.7520 S33: -0.4343
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : E 1 E 73
REMARK 3 ORIGIN FOR THE GROUP (A): 176.7764 -16.8890 20.1920
REMARK 3 T TENSOR
REMARK 3 T11: -0.0432 T22: 0.4272
REMARK 3 T33: 0.0214 T12: -0.0929
REMARK 3 T13: -0.1563 T23: 0.1144
REMARK 3 L TENSOR
REMARK 3 L11: 16.1285 L22: 5.5651
REMARK 3 L33: 7.2807 L12: -0.6302
REMARK 3 L13: 1.6985 L23: -0.5606
REMARK 3 S TENSOR
REMARK 3 S11: -0.3371 S12: 0.4914 S13: 0.9778
REMARK 3 S21: -0.5195 S22: -0.1505 S23: -0.2088
REMARK 3 S31: -0.6052 S32: 1.5821 S33: 0.4876
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : B 15 B 37
REMARK 3 ORIGIN FOR THE GROUP (A): 158.0977 -23.2462 18.7878
REMARK 3 T TENSOR
REMARK 3 T11: -0.1454 T22: -0.0350
REMARK 3 T33: -0.0561 T12: 0.0117
REMARK 3 T13: -0.1849 T23: -0.0137
REMARK 3 L TENSOR
REMARK 3 L11: 15.4757 L22: 18.8896
REMARK 3 L33: 20.8544 L12: 1.4213
REMARK 3 L13: 7.8601 L23: 4.7584
REMARK 3 S TENSOR
REMARK 3 S11: 0.5584 S12: -1.1516 S13: -0.6161
REMARK 3 S21: 1.0565 S22: -0.2998 S23: -0.4159
REMARK 3 S31: 1.0063 S32: -0.4503 S33: -0.2587
REMARK 3
REMARK 3 TLS GROUP : 5
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : D 16 D 37
REMARK 3 ORIGIN FOR THE GROUP (A): 124.7377 -25.2335 37.9852
REMARK 3 T TENSOR
REMARK 3 T11: 0.1322 T22: -0.0067
REMARK 3 T33: -0.2141 T12: 0.0893
REMARK 3 T13: 0.0012 T23: -0.1199
REMARK 3 L TENSOR
REMARK 3 L11: 16.0741 L22: 14.6495
REMARK 3 L33: 23.8676 L12: -8.9729
REMARK 3 L13: -7.1212 L23: 1.3584
REMARK 3 S TENSOR
REMARK 3 S11: 0.4279 S12: 1.9552 S13: -0.6855
REMARK 3 S21: -0.7162 S22: -0.8946 S23: 0.3395
REMARK 3 S31: 1.1757 S32: -0.8173 S33: 0.4667
REMARK 3
REMARK 3 TLS GROUP : 6
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : F 17 F 37
REMARK 3 ORIGIN FOR THE GROUP (A): 160.1725 -37.3515 38.5014
REMARK 3 T TENSOR
REMARK 3 T11: 0.1609 T22: 0.7328
REMARK 3 T33: 0.4996 T12: -0.0583
REMARK 3 T13: 0.3613 T23: -0.4671
REMARK 3 L TENSOR
REMARK 3 L11: 15.9956 L22: 18.3449
REMARK 3 L33: 7.1637 L12: 0.3561
REMARK 3 L13: -2.6207 L23: -6.6173
REMARK 3 S TENSOR
REMARK 3 S11: -1.2519 S12: 1.6056 S13: -2.1040
REMARK 3 S21: -0.0577 S22: 1.2807 S23: -0.5289
REMARK 3 S31: 0.9171 S32: 0.4716 S33: -0.0288
REMARK 3
REMARK 3 TLS GROUP : 7
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : B 38 B 73
REMARK 3 ORIGIN FOR THE GROUP (A): 139.5021 -3.8315 3.3567
REMARK 3 T TENSOR
REMARK 3 T11: -0.2649 T22: -0.4077
REMARK 3 T33: -0.2158 T12: -0.0576
REMARK 3 T13: 0.0098 T23: -0.0350
REMARK 3 L TENSOR
REMARK 3 L11: 17.8673 L22: 18.0771
REMARK 3 L33: 8.5511 L12: -14.7196
REMARK 3 L13: 8.8024 L23: -9.3934
REMARK 3 S TENSOR
REMARK 3 S11: -0.1858 S12: -0.5745 S13: 0.5482
REMARK 3 S21: 0.1340 S22: 0.3494 S23: 0.0844
REMARK 3 S31: -0.1105 S32: -0.5258 S33: -0.1636
REMARK 3
REMARK 3 TLS GROUP : 8
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : D 38 D 73
REMARK 3 ORIGIN FOR THE GROUP (A): 124.7656 -13.0281 11.3079
REMARK 3 T TENSOR
REMARK 3 T11: 0.0429 T22: 0.0057
REMARK 3 T33: 0.0013 T12: -0.0003
REMARK 3 T13: 0.0831 T23: 0.0409
REMARK 3 L TENSOR
REMARK 3 L11: 6.5677 L22: 13.4252
REMARK 3 L33: 64.5651 L12: -4.5810
REMARK 3 L13: 9.4178 L23: -22.1607
REMARK 3 S TENSOR
REMARK 3 S11: -0.3375 S12: 0.2018 S13: -0.2116
REMARK 3 S21: -0.7706 S22: 0.0530 S23: 0.3996
REMARK 3 S31: 0.8045 S32: -0.3795 S33: 0.2845
REMARK 3
REMARK 3 TLS GROUP : 9
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : F 38 F 72
REMARK 3 ORIGIN FOR THE GROUP (A): 181.4065 -29.3983 22.5921
REMARK 3 T TENSOR
REMARK 3 T11: -0.0991 T22: 0.6228
REMARK 3 T33: 0.2160 T12: 0.2099
REMARK 3 T13: -0.0447 T23: 0.0535
REMARK 3 L TENSOR
REMARK 3 L11: 20.8595 L22: 5.1876
REMARK 3 L33: 25.5132 L12: 5.0953
REMARK 3 L13: -19.2186 L23: -3.3632
REMARK 3 S TENSOR
REMARK 3 S11: -0.3138 S12: -0.0267 S13: -0.6368
REMARK 3 S21: -0.4569 S22: -0.4226 S23: -0.1877
REMARK 3 S31: 0.1902 S32: 1.4255 S33: 0.7364
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2FIF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-06.
REMARK 100 THE DEPOSITION ID IS D_1000035914.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 28-SEP-05
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSLS
REMARK 200 BEAMLINE : X12C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.2820
REMARK 200 MONOCHROMATOR : SILICON
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19257
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490
REMARK 200 RESOLUTION RANGE LOW (A) : 90.910
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59
REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 2FID
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 55.85
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 20-25% PEG 4000, 0.2M LITHIUM SULFATE
REMARK 280 , PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
REMARK 290 4555 -X+1/2,Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 96.10000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.21000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 96.10000
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.21000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 THE BIOLOGICAL ASSEMBLY IS RABEX-5 COMPLEXED WITH TWO
REMARK 300 UBIQUITIN MOLECULES. THIS CORRESPONDIS TO CHAIN B
REMARK 300 WITH CHAINS A AND E IN THE ASYMMETRIC UNIT.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1540 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 8820 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 3
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1420 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 8540 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 ARG A 74
REMARK 465 GLY A 75
REMARK 465 GLY A 76
REMARK 465 GLY B 4
REMARK 465 ALA B 5
REMARK 465 MET B 6
REMARK 465 GLY B 7
REMARK 465 SER B 8
REMARK 465 GLY B 9
REMARK 465 ILE B 10
REMARK 465 HIS B 11
REMARK 465 VAL B 12
REMARK 465 ASP B 13
REMARK 465 GLN B 14
REMARK 465 ARG C 74
REMARK 465 GLY C 75
REMARK 465 GLY C 76
REMARK 465 GLY D 4
REMARK 465 ALA D 5
REMARK 465 MET D 6
REMARK 465 GLY D 7
REMARK 465 SER D 8
REMARK 465 GLY D 9
REMARK 465 ILE D 10
REMARK 465 HIS D 11
REMARK 465 VAL D 12
REMARK 465 ASP D 13
REMARK 465 GLN D 14
REMARK 465 SER D 15
REMARK 465 ARG E 74
REMARK 465 GLY E 75
REMARK 465 GLY E 76
REMARK 465 GLY F 4
REMARK 465 ALA F 5
REMARK 465 MET F 6
REMARK 465 GLY F 7
REMARK 465 SER F 8
REMARK 465 GLY F 9
REMARK 465 ILE F 10
REMARK 465 HIS F 11
REMARK 465 VAL F 12
REMARK 465 ASP F 13
REMARK 465 GLN F 14
REMARK 465 SER F 15
REMARK 465 GLU F 16
REMARK 465 GLN F 73
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 OE1 GLN B 50 O HOH B 907 1.97
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 TRP B 31 36.01 -99.07
REMARK 500 SER B 72 -83.80 -118.37
REMARK 500 SER D 71 32.25 -65.69
REMARK 500 LEU F 18 -71.54 -86.90
REMARK 500 TRP F 31 41.87 -106.74
REMARK 500 SER F 71 -39.05 -154.98
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B 901 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS B 19 SG
REMARK 620 2 CYS B 23 SG 113.1
REMARK 620 3 CYS B 35 SG 107.8 106.3
REMARK 620 4 CYS B 38 SG 105.4 123.9 98.5
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN D 902 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS D 19 SG
REMARK 620 2 CYS D 23 SG 117.5
REMARK 620 3 CYS D 35 SG 110.8 102.7
REMARK 620 4 CYS D 38 SG 112.4 112.6 98.6
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN F 903 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS F 19 SG
REMARK 620 2 CYS F 23 SG 111.4
REMARK 620 3 CYS F 35 SG 125.4 85.3
REMARK 620 4 CYS F 38 SG 149.3 81.1 82.2
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 901
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 902
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN F 903
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 101
DBREF 2FIF A 1 76 UNP P62990 UBIQ_BOVIN 1 76
DBREF 2FIF C 1 76 UNP P62990 UBIQ_BOVIN 1 76
DBREF 2FIF E 1 76 UNP P62990 UBIQ_BOVIN 1 76
DBREF 2FIF B 9 73 UNP O18973 RABX5_BOVIN 9 73
DBREF 2FIF D 9 73 UNP O18973 RABX5_BOVIN 9 73
DBREF 2FIF F 9 73 UNP O18973 RABX5_BOVIN 9 73
SEQADV 2FIF GLY B 4 UNP O18973 INSERTION
SEQADV 2FIF ALA B 5 UNP O18973 INSERTION
SEQADV 2FIF MET B 6 UNP O18973 INSERTION
SEQADV 2FIF GLY B 7 UNP O18973 INSERTION
SEQADV 2FIF SER B 8 UNP O18973 INSERTION
SEQADV 2FIF GLY D 4 UNP O18973 INSERTION
SEQADV 2FIF ALA D 5 UNP O18973 INSERTION
SEQADV 2FIF MET D 6 UNP O18973 INSERTION
SEQADV 2FIF GLY D 7 UNP O18973 INSERTION
SEQADV 2FIF SER D 8 UNP O18973 INSERTION
SEQADV 2FIF GLY F 4 UNP O18973 INSERTION
SEQADV 2FIF ALA F 5 UNP O18973 INSERTION
SEQADV 2FIF MET F 6 UNP O18973 INSERTION
SEQADV 2FIF GLY F 7 UNP O18973 INSERTION
SEQADV 2FIF SER F 8 UNP O18973 INSERTION
SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE
SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL
SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP
SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP
SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER
SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY
SEQRES 1 B 70 GLY ALA MET GLY SER GLY ILE HIS VAL ASP GLN SER GLU
SEQRES 2 B 70 LEU LEU CYS LYS LYS GLY CYS GLY TYR TYR GLY ASN PRO
SEQRES 3 B 70 ALA TRP GLN GLY PHE CYS SER LYS CYS TRP ARG GLU GLU
SEQRES 4 B 70 TYR HIS LYS ALA ARG GLN LYS GLN ILE GLN GLU ASP TRP
SEQRES 5 B 70 GLU LEU ALA GLU ARG LEU GLN ARG GLU GLU GLU GLU ALA
SEQRES 6 B 70 PHE ALA SER SER GLN
SEQRES 1 C 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE
SEQRES 2 C 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL
SEQRES 3 C 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP
SEQRES 4 C 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP
SEQRES 5 C 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER
SEQRES 6 C 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY
SEQRES 1 D 70 GLY ALA MET GLY SER GLY ILE HIS VAL ASP GLN SER GLU
SEQRES 2 D 70 LEU LEU CYS LYS LYS GLY CYS GLY TYR TYR GLY ASN PRO
SEQRES 3 D 70 ALA TRP GLN GLY PHE CYS SER LYS CYS TRP ARG GLU GLU
SEQRES 4 D 70 TYR HIS LYS ALA ARG GLN LYS GLN ILE GLN GLU ASP TRP
SEQRES 5 D 70 GLU LEU ALA GLU ARG LEU GLN ARG GLU GLU GLU GLU ALA
SEQRES 6 D 70 PHE ALA SER SER GLN
SEQRES 1 E 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE
SEQRES 2 E 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL
SEQRES 3 E 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP
SEQRES 4 E 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP
SEQRES 5 E 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER
SEQRES 6 E 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY
SEQRES 1 F 70 GLY ALA MET GLY SER GLY ILE HIS VAL ASP GLN SER GLU
SEQRES 2 F 70 LEU LEU CYS LYS LYS GLY CYS GLY TYR TYR GLY ASN PRO
SEQRES 3 F 70 ALA TRP GLN GLY PHE CYS SER LYS CYS TRP ARG GLU GLU
SEQRES 4 F 70 TYR HIS LYS ALA ARG GLN LYS GLN ILE GLN GLU ASP TRP
SEQRES 5 F 70 GLU LEU ALA GLU ARG LEU GLN ARG GLU GLU GLU GLU ALA
SEQRES 6 F 70 PHE ALA SER SER GLN
HET SO4 A 101 5
HET ZN B 901 1
HET ZN D 902 1
HET ZN F 903 1
HETNAM SO4 SULFATE ION
HETNAM ZN ZINC ION
FORMUL 7 SO4 O4 S 2-
FORMUL 8 ZN 3(ZN 2+)
FORMUL 11 HOH *19(H2 O)
HELIX 1 1 THR A 22 GLY A 35 1 14
HELIX 2 2 PRO A 37 ASP A 39 5 3
HELIX 3 3 THR A 55 ASN A 60 5 6
HELIX 4 4 ASN B 28 GLN B 32 5 5
HELIX 5 5 CYS B 35 SER B 71 1 37
HELIX 6 6 THR C 22 GLY C 35 1 14
HELIX 7 7 PRO C 37 ASP C 39 5 3
HELIX 8 8 LEU C 56 ASN C 60 5 5
HELIX 9 9 ASN D 28 GLN D 32 5 5
HELIX 10 10 CYS D 35 ALA D 70 1 36
HELIX 11 11 THR E 22 ASP E 32 1 11
HELIX 12 12 PRO E 37 ASP E 39 5 3
HELIX 13 13 THR E 55 ASN E 60 5 6
HELIX 14 14 CYS F 35 ALA F 70 1 36
SHEET 1 A 5 THR A 12 GLU A 16 0
SHEET 2 A 5 GLN A 2 THR A 7 -1 N VAL A 5 O ILE A 13
SHEET 3 A 5 THR A 66 LEU A 71 1 O LEU A 67 N PHE A 4
SHEET 4 A 5 GLN A 41 PHE A 45 -1 N ARG A 42 O VAL A 70
SHEET 5 A 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45
SHEET 1 B 5 THR C 12 GLU C 16 0
SHEET 2 B 5 GLN C 2 THR C 7 -1 N VAL C 5 O ILE C 13
SHEET 3 B 5 THR C 66 LEU C 71 1 O LEU C 67 N PHE C 4
SHEET 4 B 5 GLN C 41 PHE C 45 -1 N ARG C 42 O VAL C 70
SHEET 5 B 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45
SHEET 1 C 5 THR E 12 GLU E 16 0
SHEET 2 C 5 GLN E 2 THR E 7 -1 N VAL E 5 O ILE E 13
SHEET 3 C 5 THR E 66 LEU E 71 1 O LEU E 67 N PHE E 4
SHEET 4 C 5 GLN E 41 PHE E 45 -1 N ILE E 44 O HIS E 68
SHEET 5 C 5 LYS E 48 GLN E 49 -1 O LYS E 48 N PHE E 45
LINK SG CYS B 19 ZN ZN B 901 1555 1555 2.33
LINK SG CYS B 23 ZN ZN B 901 1555 1555 2.29
LINK SG CYS B 35 ZN ZN B 901 1555 1555 2.33
LINK SG CYS B 38 ZN ZN B 901 1555 1555 2.38
LINK SG CYS D 19 ZN ZN D 902 1555 1555 2.42
LINK SG CYS D 23 ZN ZN D 902 1555 1555 2.37
LINK SG CYS D 35 ZN ZN D 902 1555 1555 2.53
LINK SG CYS D 38 ZN ZN D 902 1555 1555 2.31
LINK SG CYS F 19 ZN ZN F 903 1555 1555 2.88
LINK SG CYS F 23 ZN ZN F 903 1555 1555 2.88
LINK SG CYS F 35 ZN ZN F 903 1555 1555 2.55
LINK SG CYS F 38 ZN ZN F 903 1555 1555 2.86
SITE 1 AC1 4 CYS B 19 CYS B 23 CYS B 35 CYS B 38
SITE 1 AC2 4 CYS D 19 CYS D 23 CYS D 35 CYS D 38
SITE 1 AC3 4 CYS F 19 CYS F 23 CYS F 35 CYS F 38
SITE 1 AC4 4 ARG A 42 ARG A 72 LYS C 11 GLU C 34
CRYST1 192.200 44.420 69.170 90.00 108.98 90.00 C 1 2 1 12
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.005203 0.000000 0.001789 0.00000
SCALE2 0.000000 0.022512 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015288 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
